In general, a mass spectrometer comprises an ion source for generating ions from molecules to be analyzed, and ion optics for guiding the ions to a mass analyzer. A tandem mass spectrometer further comprises a second mass analyzer. In tandem mass spectrometry, structural elucidation of ionized molecules is performed by collecting a mass spectrum, then using a first mass analyzer to select a desired precursor ion or ions from the mass spectrum, causing fragmentation of the selected precursor ions, and then performing mass analysis of the fragment ions using a second mass analyzer. Generally, a mass analyzer with accurate mass capability is preferable for the second mass analyzer. It is often desirable to obtain a mass spectrum of precursor ions also using the accurate-mass mass analyzer (accurate-mass MS), i.e. pass a sample of precursor ions to the accurate-mass MS without fragmentation. The method can be extended to provide one or more further stages of fragmentation (i.e. fragmentation of fragment ions and so on). This is typically referred to as MSn, with the superscript n denoting the number of generations of ions. Thus MS2 corresponds to tandem mass spectrometry.
To properly interpret the molecular and compositional information potentially available from a tandem mass spectrometry experiment, it is desirable to be able generate fragments of various sizes, to match each fragment to the particular precursor ion from which it was produced, and to measure fragment masses with high mass accuracy (parts-per-million, ppm) and high resolution (i.e., a mass resolution of one part in 105 or better). Generation of fragments of various sizes may be accomplished by the MSn methods noted above or by performing separate fragmentation procedures (of similar precursors) at different levels of experimentally supplied energy. Matching between fragments and precursors is conventionally performed by isolating each precursor in turn for fragmentation and separately mass analyzing the fragments generated from each precursor. High resolution is generally obtained through the use of pulsed accurate-mass MS apparatuses, such as TOF analyzers, FT ICR analyzers and electrostatic trap (EST) analyzers such as the Orbitrap mass analyzer, an electrostatic trap analyzer.
Most of the accurate-mass MS apparatuses listed above have a short injection cycle followed by relatively long mass analysis stage, especially when operated at high resolution. These time requirements may be multiplied several-fold if separate mass analysis scans are required for each of several sets of fragments, each such set generated from a different precursor. Frequently, the analytes of interest are chemically complex molecules such as peptides or proteins derived from biological samples, requiring multiple fragmentations and associated analyses for unambiguous identification or characterization. Unfortunately, the analyte resolving power of modern chromatography techniques, such as high-performance liquid chromatography (HPLC) is sufficiently good that the entirety of the elution profile of an individual such analyte may last only a few seconds, from start to finish, thereby severely constraining the time available for the desired detailed analysis of precursor ions and fragment or product ions.
From the above discussion, it is evident that there is often a requirement for accurate and high resolution analysis of multiple sets of peptide fragments, from different precursors and produced at different energy levels, within tight time constraints. It is would therefore be desirable to be able to mass analyze all such precursors and fragments simultaneously, as a mixture, in a fashion that allows precursor-fragment correlation and that preserves mass resolution and accuracy. The present invention addresses such a need.